[Biojava-l] RichSequence.IOTools performance
Khalil El Mazouari
khalil.elmazouari at gmail.com
Tue Mar 29 21:47:37 UTC 2011
Hi
I am using netbeans profiler.
The total exec time was ± 20s (macbook pro i7, 4GB, SSD) for ± 10.000 seq.
By writing the RichSequence object to ByteArrayOutputStream -> FileChannel, where appropriate, the total exec time dropped to 7s. Huge improvement, for the app I am developing. The app will be used to analyze ± 100,000 sequence per run.
Regards,
khalil
On 29 Mar 2011, at 22:13, Scooter Willis wrote:
> Instead of percentage metrics can you get the time before and after the write execution for comparison without profiling. What profiler are you using?
>
>
>> On Mar 28, 2011 5:39 PM, "Andy Yates" <ayates at ebi.ac.uk> wrote:
>>
>> Dang Rich :).
>>
>> At the moment we've not done anything WRT Genbank outputting but would accept anything to help us out with this.
>>
>> As for the performance difference between BJ3 & BJ what happens if you use the writer objects directly with a BufferedOutputStream writer? Have you got any profiling results? It would be very interesting to see where we've lost the performance ...
>>
>> Andy
>>
>> On 28 Mar 2011, at 18:23, Richard Holland wrote:
>>
>> > In which case you've got little option but to r...
>>
>> --
>> Andrew Yates Ensembl Genomes Engineer
>> EMBL-EBI Tel: +44-(0)1223-492538
>> Wellcome Trust Genome Campus Fax: +44-(0)1223-494468
>> Cambridge CB10 1SD, UK http://www.ensemblgenomes.org/
>>
>>
>>
>>
>>
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